tbuckley/cabot-search huggingface dataset:
POST-IVUS: A perceptual organisation-aware selective transformer framework for intravascular ultrasound segmentation
Authors: Xingru Huang, Retesh Bajaj, Yilong Li, Xin Ye, Ji Lin, Francesca Pugliese, Anantharaman Ramasamy, Yue Gu, Yaqi Wang, Ryo Torii, Jouke Dijkstra, Huiyu Zhou, Christos V. Bourantas, Qianni Zhang
Journal: Medical Image Analysis (2023)

Intravascular ultrasound (IVUS) is recommended in guiding coronary intervention. The segmentation of coronary lumen and external elastic membrane (EEM) borders in IVUS images is a key step, but the manual process is time-consuming and error-prone, and suffers from inter-observer variability. In this paper, we propose a novel perceptual oganisation-aware selective transformer framework that can achieve accurate and robust segmentation of the vessel walls in IVUS images. In this framework, temporal context-based feature encoders extract efficient motion features of vessels. Then, a perceptual oganisation-aware selective transformer module is proposed to extract accurate boundary information, supervised by a dedicated boundary loss. The obtained EEM and lumen segmentation results will be fused in a temporal constraining and fusion module, to determine the most likely correct boundaries with robustness to morphology. Our proposed methods are extensively evaluated in non-selected IVUS sequences, including normal, bifurcated, and calcified vessels with shadow artifacts. The results show that the proposed methods outperform the state-of-the-art, with a Jaccard measure of 0.92 for lumen and 0.94 for EEM on the IVUS 2011 open challenge dataset. This work has been integrated into a software QCU-CMS2 to automatically segment IVUS images in a user-friendly environment.
Hemophagocytic lymphohistiocytosis–like hyperinflammation due to a de novo mutation in DPP9
Authors: Christine Wolf, Hannah Fischer, Jörn-Sven Kühl, Sarah Koss, Rami Abou Jamra, Sven Starke, Jurek Schultz, Stephan Ehl, Katrin Neumann, Catharina Schuetz, Robert Huber, Veit Hornung, Min Ae Lee-Kirsch
Journal: Journal of Allergy and Clinical Immunology (2023)
Differences and similarities between the EULAR/ASAS-EULAR and national recommendations for treatment of patients with psoriatic arthritis and axial spondyloarthritis across Europe
Authors: Brigitte Michelsen, Mikkel Østergaard, Michael John Nissen, Adrian Ciurea, Burkhard Möller, Lykke Midtbøll Ørnbjerg, Jakub Zavada, Bente Glintborg, Alan MacDonald, Karin Laas, Dan Nordström, Bjorn Gudbjornsson, Florenzo Iannone, Pasoon Hellmand, Tore Kristian Kvien, Ana Maria Rodrigues, Catalin Codreanu, Ziga Rotar, Isabel Castrejón Fernández, Johan Karlsson Wallman, Jiri Vencovsky, Anne Gitte Loft, Maureen Heddle, Sigrid Vorobjov, Anna-Mari Hokkanen, Gerdur Gröndal, Marco Sebastiani, Marleen van de Sande, Eirik Klami Kristianslund, Maria José Santos, Corina Mogosan, Matija Tomsic, Federico Díaz-González, Daniela Di Giuseppe, Merete Lund Hetland
Journal: The Lancet Regional Health - Europe (2023)

This is the first report comparing EULAR and national treatment recommendations for PsA patients across Europe, and the first this decade to compare ASAS-EULAR and national treatment recommendations in axSpA patients. An electronic survey was completed from October 2021–April 2022 by rheumatologists in 15 European countries. One and four countries followed all EULAR and ASAS-EULAR recommendations, respectively. Five countries had no national treatment recommendations for PsA and/or axSpA, but followed other regulations. In several countries, national treatment recommendations predated the most recent EULAR/ASAS-EULAR recommendations. Entry criteria for starting biologic/targeted synthetic disease-modifying anti-rheumatic drugs varied considerably. In several countries, for PsA patients with significant skin involvement, interleukin-17 inhibitors were not given preference. The positioning of Janus Kinase inhibitors differed and Phosphodiesterase-4 inhibitors were not in use/reimbursed in most countries. This study may motivate European countries to update their national treatment recommendations, to align them better with the latest international recommendations.
Coats-like Vasculopathy in Inherited Retinal Disease
Authors: Malena Daich Varela, Giovanni Marco Conti, Samantha Malka, Veronika Vaclavik, Omar A. Mahroo, Andrew R. Webster, Viet Tran, Michel Michaelides
Journal: Ophthalmology (2023)

PurposeTo describe the largest, most phenotypically and genetically diverse cohort of patients with inherited retinal disease (IRD)-related Coats-like vasculopathy (CLV).DesignMulticentre retrospective cohort study.Subjects67 patients with IRD-related CLVMethodsReview of clinical notes, ophthalmic imaging, and molecular diagnosis from two international centres.Main outcome measuresVisual function, retinal imaging, management and response to treatment were evaluated and correlated.ResultsThe prevalence of IRD-related CLV was 0.5%; 55% of patients had isolated retinitis pigmentosa (RP), 21% had early onset severe retinal dystrophy, and less frequent presentations were syndromic RP, sector RP, cone-rod dystrophy, achromatopsia, PAX6-related dystrophy, and X-linked retinoschisis. The overall age of CLV diagnosis was 30.7 ± 16.9 years old (1 – 83). Twenty-one patients (31%) had unilateral CLV and the most common retinal features were telangiectasia, exudates, and exudative retinal detachment (ERD) affecting the inferior and temporal retina. Macular oedema/schisis was seen in 26% of the eyes and ERD in 63%. Fifty-four patients (81%) had genetic testing, 40 of whom were molecularly solved.Sixty-six eyes (58%) were observed, 17 (15%) were treated with a single modality, and 30 (27%) had a combined approach. Thirty-five eyes (31%) were 'good responders', 42 (37%) were 'poor responders', 22 (19%) had low vision at baseline and were only observed, and 12 (11%) did not have longitudinal assessment. Twenty-one (62%) observed eyes responded well, versus 14 (33%) treated eyes. Final best-corrected visual acuity (BCVA) was significantly worse than baseline (p 0.002); 40 patients (60%) lost 15 ETDRS letters or more over follow up in one or both eyes, and 21 patients (31%) progressed to more advanced stages of visual impairment.ConclusionsIRD-related CLV is rare, sporadic, mostly bilateral, no gender predominant, and can occur in diverse types of IRD at any point of the disease, with a mean onset in the fourth decade of life. Patients with IRD-related CLV who have decreased initial VA, ERD, CLV changes affecting two or more retinal quadrants, and CRB1-retinopathy may be at higher risk of a poor prognosis.
Impact of Breast Cancer Screening on 10-Year Net Survival in Canadian Women Age 40-49 Years
Authors: Anna N. Wilkinson, Larry F. Ellison, Jean-Michel Billette, Jean M. Seely
Journal: Journal of Clinical Oncology (2023)

In Canada, some provincial/territorial mammography screening programs include women age 40-49 years, whereas others do not. This study examines the impact of this dichotomy on the 10-year breast cancer (BC) net survival (NS) among women age 40-49 years and 50-59 years at diagnosis.Using the Canadian Cancer Registry data record linked to death information, we evaluated the cohort of Canadian women age 40-49 years and 50-59 years diagnosed with BC from 2002 to 2007. We compared 10-year NS estimates in the jurisdictions with organized screening programs that included women age 40-49 years, designated as screeners (Northwest Territories, British Columbia, Alberta, Nova Scotia, and Prince Edward Island), with comparator programs that did not (Yukon, Manitoba, Saskatchewan, Ontario, Quebec, New Brunswick, and Newfoundland and Labrador).BC was the primary cause of 10-year mortality in women age 40-49 years diagnosed with BC (90.7% of deaths). Among these women, the 10-year NS for screeners (84.8%; 95% CI, 83.8 to 85.8) was 1.9 percentage points (pp) higher than that for comparators (82.9%; 95% CI, 82.3 to 83.5; P = .001). The difference in favor of screeners was significant among women age 45-49 years (2.6 pp; P = .001) but not among women age 40-44 years (0.9 pp; P = .328). Similarly, the incidence-based BC mortality rate was significantly lower in screener jurisdictions among women age 40-49 years and 45-49 years, but not for 40-44 years. Provincial/territorial NS increased significantly with higher mammography screening participation (P = .003). The BC incidence rate was virtually identical in screener and comparator jurisdictions among women age 40-49 years (P = .976) but was significantly higher for comparators among women age 50-59 years (P < .001).Screening programs that included women in their 40s were associated with a significantly higher BC 10-year NS in women age 40-49 years, but not an increased rate of BC diagnosis. These results may inform screening guidelines for women age 40-49 years.
Optimizing Lung Cancer Screening With Risk Prediction: Current Challenges and the Emerging Role of Biomarkers
Authors: Julie Tsu-yu Wu, Heather A. Wakelee, Summer S. Han
Journal: Journal of Clinical Oncology (2023)

Lung cancer screening has been demonstrated to reduce lung cancer mortality, but its benefits must be weighed against the potential harms of unnecessary procedures, false-positive radiological findings, and overdiagnosis. Individuals at highest risk of lung cancer are more likely to maximize benefits while minimizing harm from screening. Although current lung cancer screening guidelines recommended by the US Preventive Services Task Force (USPSTF) only consider age and smoking history for screening eligibility, National Comprehensive Cancer Network and other society guidelines recommend screening on the basis of individualized risk assessment including family history, environmental exposures, and presence of chronic lung disease. Risk prediction models have been developed to integrate various risk factors into an individualized risk prediction score. Previous evidence showed that risk prediction model-based screening eligibility could improve sensitivity for detecting lung cancer cases without reducing specificity. Furthermore, recent advances in lung cancer biomarkers have enhanced the performance of risk prediction in identifying lung cancer cases relative to the USPSTF criteria. These risk prediction models can be used to guide shared decision-making discussions before proceeding with lung cancer screening. This study aims to provide a concise overview of these prediction models and the emerging role of biomarker testing in risk prediction to facilitate conversations with patients. The goal was to assist clinicians in assessing individual patient risk, leading to more informed decision making.
A nano-conductive osteogenic hydrogel to locally promote calcium influx for electro-inspired bone defect regeneration
Authors: Congcong Yu, Xiaozhang Ying, Mohammad-Ali Shahbazi, Linjun Yang, Zaiqiang Ma, Lin Ye, Wentao Yang, Rongtai Sun, Tianyuan Gu, Ruikang Tang, Shunwu Fan, Shasha Yao
Journal: Biomaterials (2023)
When I use a word . . . Preventable deaths and public awareness
Authors: Jeffrey K Aronson
Journal: BMJ (2023)

Coroners in England and Wales have a duty to write reports highlighting factors that they think may have contributed to deaths, asking for action from those who might be able to reduce the risks of further deaths from the same causes. These reports are known as Prevent Future Deaths reports or PFDs. Analyses of the reports themselves and of papers published about them in peer reviewed journals and of accounts published in <i>The BMJ</i> and national newspapers suggest that these reports could be more widely circulated. The Preventable Deaths Tracker, freely available online, aims to encourage greater public awareness of PFDs and more research into the lessons they contain.
17th International Conference on Malignant Lymphoma: Key Takeaways
Journal: Blood Cancer Discovery (2023)

Abstract The 17th International Conference on Malignant Lymphoma (ICML) took place in Lugano, Switzerland, from June 13–17 this year. The conference has been held every 2 to 3 years since its inception in 1981 and has become a significant and influential gathering for lymphoma researchers from around the world, this year hosting 4,761 registered attendees. Here, we provide some highlights of what we felt were the most noteworthy findings, both clinical and pre-clinical, across various lymphoma entities, presented at the 17th ICML.
Reactive Oxygen Species‐Responsive Polymeric Prodrug Nanoparticles for Selective and Effective Treatment of Inflammatory Diseases
Authors: Yaming Zhang, Lu Liu, Tianyi Wang, Cong Mao, Pengfei Shan, Chak Sing Lau, Zhongyu Li, Weisheng Guo, Weiping Wang
Journal: Advanced Healthcare Materials (2023)

It is challenging to manage inflammatory diseases using traditional anti-inflammatory drugs due to their limited efficacy and systemic side effects, which are a result of their lack of selectivity, poor stability, and low solubility. Herein, it reports the development of a novel nanoparticle system, called ROS-CA-NPs, which is formed using polymer-cinnamaldehyde (CA) conjugates and is responsive to reactive oxygen species (ROS). ROS-CA-NPs exhibit excellent drug stability, tissue selectivity, and controlled drug release upon oxidative stress activation. Using mouse models of chronic rheumatoid arthritis and acute ulcerative colitis, this study demonstrates that the systemic administration of ROS-CA-NPs results in their accumulation at inflamed lesions and leads to greater therapeutic efficacy compared to traditional drugs. Furthermore, ROS-CA-NPs present excellent biocompatibility. The findings suggest that ROS-CA-NPs have the potential to be developed as safe and effective nanotherapeutic agents for a broad range of inflammatory diseases.
Conformation Dependent Architectures of Assembled Antimicrobial Peptides with Enhanced Antimicrobial Ability
Authors: Xinmiao Lan, Jie Zhong, Regina Huang, Yuhan Liu, Xiaowei Ma, Xuan Li, Dan Zhao, Guangchao Qing, Yuxuan Zhang, Lu Liu, Jinjin Wang, Xu Ma, Ting Luo, Weisheng Guo, Yuji Wang, Li‐Li Li, Yu‐Xiong Su, Xing‐Jie Liang
Journal: Advanced Healthcare Materials (2023)

Antimicrobial peptides (AMPs) are a developing class of natural and synthetic oligopeptides with host defense mechanisms against a broad spectrum of microorganisms. With in-depth research on the structural conformations of AMPs, synthesis or modification of peptides has shown great potential in effectively obtaining new therapeutic agents with improved physicochemical and biological properties. Notably, AMPs with self-assembled properties have gradually become a hot research topic for various biomedical applications. Compared to monomeric peptides, these peptides can exist in diverse forms (e.g., nanoparticles, nanorods, and nanofibers) and possess several advantages, such as high stability, good biocompatibility, and potent biological functions, after forming aggregates under specific conditions. In particular, the stability and antibacterial property of these AMPs can be modulated by rationally regulating the peptide sequences to promote self-assembly, leading to the reconstruction of molecular structure and spatial orientation while introducing some peptide fragments into the scaffolds. In this work, four self-assembled AMPs are developed, and the relationship between their chemical structures and antibacterial activity is explored extensively through different experiments. Importantly, the evaluation of antibacterial performance in both in vitro and in vivo studies has provided a general guide for using self-assembled AMPs in subsequent treatments for combating bacterial infections.
Comparative antibody and cell-mediated immune responses, reactogenicity, and efficacy of homologous and heterologous boosting with CoronaVac and BNT162b2 (Cobovax): an open-label, randomised trial
Authors: Nancy H L Leung, Samuel M S Cheng, Carolyn A Cohen, Mario Martín-Sánchez, Niki Y M Au, Leo L H Luk, Leo C H Tsang, Kelvin K H Kwan, Sara Chaothai, Lison W C Fung, Alan W L Cheung, Karl C K Chan, John K C Li, Yvonne Y Ng, Prathanporn Kaewpreedee, Janice Z Jia, Dennis K M Ip, Leo L M Poon, Gabriel M Leung, J S Malik Peiris, Sophie A Valkenburg, Benjamin J Cowling
Journal: The Lancet Microbe (2023)

Few trials have compared homologous and heterologous third doses of COVID-19 vaccination with inactivated vaccines and mRNA vaccines. The aim of this study was to assess immune responses, safety, and efficacy against SARS-CoV-2 infection following homologous or heterologous third-dose COVID-19 vaccination with either one dose of CoronaVac (Sinovac Biotech; inactivated vaccine) or BNT162b2 (Fosun Pharma-BioNTech; mRNA vaccine).
Update on the Porphyrias
Authors: Amy K. Dickey, Rebecca Karp Leaf, Manisha Balwani
Journal: Annual Review of Medicine (2023)

The porphyrias are a group of rare diseases, each resulting from a defect in a different enzymatic step of the heme biosynthetic pathway. They can be broadly divided into two categories, hepatic and erythropoietic porphyrias, depending on the primary site of accumulation of heme intermediates. These disorders are multisystemic with variable symptoms that can be encountered by physicians in any specialty. Here, we review the porphyrias and describe their clinical presentation, diagnosis, and management. We discuss novel therapies that are approved or in development. Early diagnosis is key for the appropriate management and prevention of long-term complications in these rare disorders.
Neuro-ophthalmology Emergency Department and Inpatient Consultations at a Large Academic Referral Center
Authors: Avital Lily Okrent Smolar, Hetal J. Ray, Michael Dattilo, Walid Bouthour, Gabriele Berman, Jason H. Peragallo, Sachin Kedar, Andrew M. Pendley, James G. Greene, Matthew T. Keadey, David W. Wright, Beau B. Bruce, Nancy J. Newman, Valérie Biousse
Journal: Ophthalmology (2023)
Impact of beta-blockers on mortality and cardiovascular disease outcomes in patients with obstructive sleep apnoea: a population-based cohort study in target trial emulation framework
Authors: Anthony Chen, Chengsheng Ju, Isla S. Mackenzie, Thomas M. MacDonald, Allan D. Struthers, Li Wei, Kenneth K.C. Man
Journal: The Lancet Regional Health - Europe (2023)

There is no real-world evidence regarding the association between beta-blocker use and mortality or cardiovascular outcomes in patients with obstructive sleep apnoea (OSA). We aimed to investigate the impact of beta-blocker use on all-cause mortality and cardiovascular diseases (CVDs) in patients with OSA.We conducted a target trial emulation study of 37,581 patients with newly diagnosed OSA from 1st January 2000 to 30th November 2021 using the IMRD-UK database (formerly known as the THIN database). We compared the treatment strategies of initiating beta-blocker treatment within one year versus non-beta-blocker treatment through the method of clone-censor-weight. Covariates, including patients' demographics, lifestyle, comorbidities, and recent medications, were measured and controlled. Patients were followed up for all-cause mortality or composite CVD outcomes (angina, myocardial infarction, stroke/transient ischaemic attack, heart failure, or atrial fibrillation). We estimated the five-year absolute risks, risk differences and risk ratio with 95% confidence intervals (CIs) with standardised, weighted pooled logistic regression, which is a discrete-time hazard model for survival analysis. Several sensitivity analyses were performed, including multiple imputation addressing the missing data.The median follow-up time was 4.1 (interquartile range, 1.9-7.8) years. The five-year absolute risk of all-cause mortality and CVD outcomes were 4.9% (95% CI, 3.8-6.0) and 13.0% (95% CI, 11.4-15.0) among beta-blocker users, and 4.0% (95% CI, 3.8-4.2) and 9.4% (95% CI, 9.1-9.7) among non-beta-blocker users, respectively. The five-year absolute risk difference and risk ratio between the two groups for all-cause mortality and CVD outcomes were 0.9% (95% CI, -0.2 to 2.1) and 1.22 (95% CI, 0.96-1.54), and 3.5% (95% CI, 2.1-5.5) and 1.37 (95% CI, 1.22-1.62), respectively. Findings were consistent across the sensitivity analyses.Beta-blocker treatment was associated with an increased risk of CVD and a trend for an increased risk of mortality among patients with OSA. Further studies are needed to confirm our findings.Innovation and Technology Commission of the Hong Kong Special Administration Region Government.
Enolase represents a metabolic checkpoint controlling the differential exhaustion programmes of hepatitis virus-specific CD8<sup>+</sup>T cells
Authors: Frances Winkler, Anna V Hipp, Carlos Ramirez, Bianca Martin, Matteo Villa, Emilia Neuwirt, Oliver Gorka, Jeroen Aerssens, Susanne E Johansson, Nisha Rana, Sian Llewellyn-Lacey, David A Price, Marcus Panning, Olaf Groß, Erika L Pearce, Carl M Hermann, Kathrin Schumann, Luciana Hannibal, Christoph Neumann-Haefelin, Tobias Boettler, Percy Knolle, Maike Hofmann, Dirk Wohlleber, Robert Thimme, Bertram Bengsch
Journal: Gut (2023)

Exhausted T cells with limited effector function are enriched in chronic hepatitis B and C virus (HBV and HCV) infection. Metabolic regulation contributes to exhaustion, but it remains unclear how metabolism relates to different exhaustion states, is impacted by antiviral therapy, and if metabolic checkpoints regulate dysfunction.Metabolic state, exhaustion and transcriptome of virus-specific CD8+ T cells from chronic HBV-infected (n=31) and HCV-infected patients (n=52) were determined ex vivo and during direct-acting antiviral (DAA) therapy. Metabolic flux and metabolic checkpoints were tested in vitro. Intrahepatic virus-specific CD8+ T cells were analysed by scRNA-Seq in a HBV-replicating murine in vivo model of acute and chronic infection.HBV-specific (core18-27, polymerase455-463) and HCV-specific (NS31073-1081, NS31406-1415, NS5B2594-2602) CD8+ T cell responses exhibit heterogeneous metabolic profiles connected to their exhaustion states. The metabolic state was connected to the exhaustion profile rather than the aetiology of infection. Mitochondrial impairment despite intact glucose uptake was prominent in severely exhausted T cells linked to elevated liver inflammation in chronic HCV infection and in HBV polymerase455-463 -specific CD8+ T cell responses. In contrast, relative metabolic fitness was observed in HBeAg-negative HBV infection in HBV core18-27-specific responses. DAA therapy partially improved mitochondrial programmes in severely exhausted HCV-specific T cells and enriched metabolically fit precursors. We identified enolase as a metabolic checkpoint in exhausted T cells. Metabolic bypassing improved glycolysis and T cell effector function. Similarly, enolase deficiency was observed in intrahepatic HBV-specific CD8+ T cells in a murine model of chronic infection.Metabolism of HBV-specific and HCV-specific T cells is strongly connected to their exhaustion severity. Our results highlight enolase as metabolic regulator of severely exhausted T cells. They connect differential bioenergetic fitness with distinct exhaustion subtypes and varying liver disease, with implications for therapeutic strategies.